The currently accepted scientific name of Baker cypress is Cupressus bakeri Jeps. There are no recognized hybrids, varieties, or forms although two subspecies are recognized by some authors: Cupressus bakeri ssp. bakeri Jeps. -- Baker or Modoc CypressCupressus bakeri ssp. matthewsii Wolf -- Siskiyou Cypress

Dodd and Rafii (1994) assert that population studies of morphological and chemical diversity in Cupressus bakeri do not support the segregation of subspecies.

Justification:This species is known from less than 10 locations, with the largest subpopulation covering less than 3 km². Calculating the AOO based on mapping herbarium collections and using the IUCN recommended 2×2 km grid size, and observing or inferring a continuous decline in numbers of mature trees, this species meets the criteria under B2 for Endangered.

This species is known from nine scattered sites in northern California and the extreme south of Oregon. Only one of them extends as far as two miles in length. Locations once known have been lost. In northern California C. bakeri occurs in Siskiyou, Modoc, Shasta, Plumas and Tehama Counties; and in southwest Oregon it is very localized in Josephine and Jackson Counties. This includes locales in the Modoc Plateau, southern Cascade Range, Klamath Mountains, Siskiyou Mts. and northern Sierra Nevada.

Fire suppression policies have reduced numbers of Cupressus bakeri. A population on ‘the North fork of the South fork of Cow Creek’ (Sudworth 1908) was described in a letter from J. C. La Plant to Sudworth in 1908 but this population now seems to be extinct. The largest existing subpopulation sprawls over 2.8 km² of basalt near Timbered Crater. Most subpopulations are much smaller and also scattered, some are quite disjunct.

Baker Cypress is a component of the northern interior cypress forest. This habitat type is an open, fire-maintained, scrubby forest. It is associated with serpentine chaparral, and intergrades on less severe sites with upper Sonoran mixed chaparral, montane chaparral, or knobcone pine forest community types. On more mesic sites, the northern interior cypress forest intergrades with mixed evergreen forest or montane coniferous forest. Baker Cypress rarely forms pure stands. The Timbered Crater grove is associated with yellow pine (Pinus ponderosa and P. jeffreyi) forest and suggests a transition zone between several plant communities, including northern juniper woodland, yellow pine forest, and sagebrush scrub. High elevation groves of Baker Cypress in Plumas County, California, are associated with Red Fir (Abies magnifica) Forest. In the Siskiyou Mountains, Baker Cypress occurs on serpentine soils; in the Sierra Nevada and Cascade Range it occurs on basic volcanic rock.

Baker Cypress reproduces exclusively from seed. Cone production is abundant. Staminate cones are produced on trees that are 6 to 7 years old. Ovulate cones are produced on trees that are 14 years of age or older and require 2 years to mature. They contain from 50 to 100 seeds per cone. The cones are closed; they persist on the tree until opened by the heat of a fire or desiccation due to age. Seeds are shed gradually over several months after the cones are opened by heat. Detached cones will open, but they rarely result in seedling establishment, usually due to the lack of a suitable seedbed. Seed dispersal is primarily by wind and rain.

Baker Cypress requires bare mineral soil for germination and seedling establishment. Seedlings of Baker Cypress have been found in areas that do not show signs of recent fire, but the seedlings are usually in the immediate vicinity of fallen cypress trees and along skid roads. Seedling mortality is greater in shaded situations with abundant litter because of damping-off. Seedlings are sensitive to excessive moisture. Baker Cypress is restricted to well-drained soils. Soil profiles are almost absent. On gentle slopes trees can be found on deeper soil profiles.

Pollen is shed in late fall, winter, and spring. Seeds mature 15 to 18 months after pollination. Ovulate cones ripen the second season after pollination, but remain closed until opened by heat or age.

Baker Cypress is a fire-adapted, fire-dependent species. Reproduction is usually restricted to burned sites. The serotinous cones of Baker Cypress persist on the trees for years. Cone-opening is erratic, slow, and almost negligible except when cones are exposed to extreme heat; then it is rapid and uniform. When opened by the heat of a fire, the seeds fall on exposed mineral soil, and produce thickets of seedlings. Most seed falls in the first few months following fire. Fires that occur in late summer and fall, followed by winter rains, ensure seed dissemination on bare mineral substrates.

No commercial uses are known of this species; like other cypresses trees may have been felled for fence posts in the past. Although trees retain a conical crown which is attractive in gardens, it is little used in horticulture, presumably because it is not strikingly distinct from other Californian species.

Fires occurring too frequently in cypress groves may destroy them, as reproduction could be eliminated before it had a chance to produce cones. Conversely, fire suppression could threaten the species. Fire suppression policies of the past decades have severely limited reproduction of this fire dependent species. In the Mud Lake-Wheeler Peak area of Plumas County, CA, Baker Cypress is being replaced by Red and White Firs (Abies magnifica, A. concolor). Hundreds of saplings and pole-sized trees have died with no indication of insects or disease. Competition of crowns for light, shading of the ground, and accumulation of thick, black duff characteristic of dense true fir stands have created an unfavourable environment for the establishment and survival of Baker Cypress. Most cypresses of California are very sensitive to lack of light, losing their foliage when growing in shade.

Seedlings of Baker Cypress are susceptible to damping-off fungi. Baker Cypress is occasionally attacked by Juniper Mistletoe (Phoradendron juniperinum ssp. juniperinum) in Plumas County, and Siskiyou Cypress (C. bakeri ssp. matthewsii) has been infected by Coryneum Canker (Coryneum cardinale), which can kill trees.

Cupressus bakeri is present in several protected areas. Management of fire, such that it is allowed to occur at frequencies and intensities approaching the natural situation, is paramount to the conservation of this species. In the absence of fire more subpopulations will be outcompeted by other conifers.